1. A myGrid Project Tutorial
Dr Mark Greenwood
University of Manchester
With considerable help from Justin Ferris, Peter Li, Phil Lord, Chris Wroe, Carole Goble and the rest of the myGrid team.

2. Open Source Upper Middleware for Bioinformatics
(Web) Service-based architecture
Targeted at Tool Developers, Bioinformaticians and Service Providers
Newcastle
Sheffield
Manchester
Nottingham
Hinxton
Southampton

3. myGrid People
Core
Matthew Addis, Nedim Alpdemir, Tim Carver, Rich Cawley, Neil Davis, Alvaro Fernandes, Justin Ferris, Robert Gaizaukaus, Kevin Glover, Carole Goble, Chris Greenhalgh, Mark Greenwood, Yikun Guo, Ananth Krishna, Peter Li, Phillip Lord, Darren Marvin, Simon Miles, Luc Moreau, Arijit Mukherjee, Tom Oinn, Juri Papay, Savas Parastatidis, Norman Paton, Terry Payne, Matthew Pockock Milena Radenkovic, Stefan Rennick-Egglestone, Peter Rice, Martin Senger, Nick Sharman, Robert Stevens, Victor Tan, Anil Wipat, Paul Watson and Chris Wroe.
Users
Simon Pearce and Claire Jennings, Institute of Human Genetics School of Clinical Medical Sciences, University of Newcastle, UK
Hannah Tipney, May Tassabehji, Andy Brass, St Mary’s Hospital, Manchester, UK
Postgraduates
Martin Szomszor, Duncan Hull, Jun Zhao, Pinar Alper, John Dickman, Keith Flanagan, Antoon Goderis, Tracy Craddock, Alastair Hampshire
Industrial
Dennis Quan, Sean Martin, Michael Niemi, Syd Chapman (IBM)
Robin McEntire (GSK)
Collaborators
Keith Decker

4. Roadmap - start
services
data

5. Tenet I
High level Middleware services for data intensive resource interoperation for Bioinformatics
Information Grid not computational Grid
Exploratory, ad hoc
For individuals
In silico experiment as workflow
Distributed query processing
Information Management

6. Tenet II High level services for e-Science experimental management;
Provenance
Event notification
Personalisation
Sharing knowledge and sharing components
Scientific discovery is personal & global.
Federated third party registries for workflows and services
Workflow and service discovery for reuse and repurposing
Find
Annotate
Registry
Register

7. Tenet III Open Source and Open Services
No control or influence over service providers
Open to third party metadata and services
Open extensible architecture
Assemble your own components
Designed to work together
Toolkit
Freefluo
WfEE
Taverna
View
UDDI
registry
Event
Notification
mIR
Pedro
Semantic
Discovery
Info.
Model
Soaplab
Gateway
& Portal
LSID
Haystack
Provenance
Browser
Openness
open source
open world of services
open extensible technology
open to wider eScience context
open to user feedback
open to third party metadata
Collection of components for assembly
Pick and mix

8. Tenet IV (Web) Service architecture Metadata driven
Publication, discovery, interoperation, composition, decommissioning of myGrid services
WS-I -> OGSA / WSRF
Metadata driven
Ontologies
Common information model
Semantic Web technologies
RDF, OWL

9. Tenet V Middleware for Tool Developers Bioinformaticians
Service Providers
Biologists are indirectly supported by the portals and apps these develop.
In silico experiments are workflows (see other talks)

10. Roadmap services workflows workflows data discover services
run workflows
data
data management

11. Data-intensive bioinformatics
Bioinformatics analyses typically involve visiting many data resources and analytical tools
ID MURA_BACSU STANDARD; PRT; AA.
DE PROBABLE UDP-N-ACETYLGLUCOSAMINE 1-CARBOXYVINYLTRANSFERASE
DE (EC ) (ENOYLPYRUVATE TRANSFERASE) (UDP-N-ACETYLGLUCOSAMINE
DE ENOLPYRUVYL TRANSFERASE) (EPT).
GN MURA OR MURZ.
OS BACILLUS SUBTILIS.
OC BACTERIA; FIRMICUTES; BACILLUS/CLOSTRIDIUM GROUP; BACILLACEAE;
OC BACILLUS.
KW PEPTIDOGLYCAN SYNTHESIS; CELL WALL; TRANSFERASE.
FT ACT_SITE BINDS PEP (BY SIMILARITY).
FT CONFLICT S -> A (IN REF. 3).
SQ SEQUENCE AA; MW; C5C CRC32;
MEKLNIAGGD SLNGTVHISG AKNSAVALIP ATILANSEVT IEGLPEISDI ETLRDLLKEI
GGNVHFENGE MVVDPTSMIS MPLPNGKVKK LRASYYLMGA MLGRFKQAVI GLPGGCHLGP
RPIDQHIKGF EALGAEVTNE QGAIYLRAER LRGARIYLDV VSVGATINIM LAAVLAEGKT
IIENAAKEPE IIDVATLLTS MGAKIKGAGT NVIRIDGVKE LHGCKHTIIP DRIEAGTFMI

12. Use Scenarios Graves’ Disease Williams-Beuren Syndrome
Autoimmune disease of the thyroid
Simon Pearce and Claire Jennings, Institute of Human Genetics School of Clinical Medical Sciences, University of Newcastle
Discover all you can about a gene
Annotation pipelines and Gene expression analysis
Services from Japan, Hong Kong, various sites in UK
Williams-Beuren Syndrome
Microdeletion of 155 Mbases on Chromosome 7
Hannah Tipney, May Tassabehji, Andy Brass, St Mary’s Hospital, Manchester, UK
Characterise an unknown gene
Annotation pipelines and Gene expression analysis Services from USA, Japan, various sites in UK

13. Manually filling a genomic gap
Two major steps:
Extend into the gap: Similarity searches; RepeatMasker, BLAST
Characterise the new sequence: NIX, Interpro, etc…
Numerous web-based services (i.e. BLAST, RepeatMasker)
Cutting and pasting between screens
Large number of steps
Frequently repeated – info now rapidly added to public databases
Don’t always get results
Time consuming
Huge amount of interrelated data is produced – handled in lab book and files saved to local hard drive
Mundane
Much knowledge remains undocumented
Bioinformatician does the analysis

14. WBS Workflows: Query nucleotide sequence RepeatMasker ncbiBlastWrapper
Pink: Outputs/inputs of a service
Purple: Taylor-made services
Green: Emboss soaplab services
Yellow: Manchester soaplab services
Grey: Unknowns
WBS Workflows:
GenBank Accession No
URL inc GB identifier
Translation/sequence file. Good for records and publications
prettyseq
GenBank Entry
Amino Acid translation
Identifies PEST seq
Sort for appropriate Sequences only
epestfind
6 ORFs
Identifies FingerPRINTS
Seqret
pscan
MW, length, charge, pI, etc
pepstats
Nucleotide seq (Fasta)
sixpack
Predicts Coiled-coil regions
ORFs
transeq
pepcoil
RepeatMasker
tblastn Vs nr, est, est_mouse, est_human databases.
Blastp Vs nr
Coding sequence
GenScan
ncbiBlastWrapper
Restriction enzyme map
SignalP
TargetP
PSORTII
restrict
Predicts cellular location
CpG Island locations and %
cpgreport
Identifies functional and structural domains/motifs
InterPro
PFAM
Prosite
Smart
RepeatMasker
Repetative elements
Hydrophobic regions
Pepwindow?
Octanol?
ncbiBlastWrapper
Blastn Vs nr, est databases.

15. Graves’ Disease Bioinformatics
Peter Li1, Claire Jennings2, Simon Pearce2 and Anil Wipat1, (2003)
1School of Computing Science and 2Institute of Human Genetics,
University of Newcastle-upon-Tyne.
Candidate gene
pool
Graves’ Disease Bioinformatics
Annotation Pipeline
Genotype Assay Design System
3D Protein Structure
What is known about my
candidate gene?
Is this SNP present
in my samples?
What is the structure of the protein
product encoded by my candidate gene?
Medline
Gene ID
PDB
Query PDB & display protein
structure
Primer Design
EMBL GO
Emboss Eprimer application
in SoapLab
Use primers designed by myGrid
to amplify region flanking SNP on the gene
Obtain information about protein
& extract information about active site
Swiss-Prot
AMBIT
Interpro
SNP
Query
Restriction Fragment
Length Polymorphism experiment
OMIM
BLAST
AMBIT
Determine whether coding SNP
affects the active site of the protein
Selection of restriction enzyme
Emboss Restrict
in SoapLab
Talisman
DQP SN
SNP P SN P

16. Experiment life cycle Forming experiments Personalisation
Discovering and reusing
experiments and resources
Executing and monitoring experiments
Sharing
services & experiments
Managing lifecycle, provenance and results of experiments

17. (e-)Scientists… …Experiment …Analyze …Collaborate …Publish …Review
Can workflow be used as an experimental method?
How many times has this experiment been run?
…Analyze
How do we manage the results to draw conclusions from them?
How reliable are these results?
…Collaborate
Can we share workflows, results, metadata etc?
…Publish
Can we link to these workflows and results from our papers?
…Review
Can I find, comprehend and review your work?
How was that result derived?

18. Collections of Tasks Building Domain Tasks Workflow Enactment Storage
Service
Providers
Enactment
Bioinformaticians
Storage
Scientists
Description
Provenance
Service
Discovery
Data
Management
Finding
Querying
Annotation
providers

19. Registry Bioinformaticians Taverna WF Builder Discovery View FreeFluo
Querying/sharing/
federating/registering
Query &
Retrieve
Workflow
Execution
Annotation/description
Discovery View
FreeFluo
Enactor
invoking
Annotation
providers
Interface
Description
Store data/
knowledge
Pedro
Annotation tool
mIR
Others
Service
Providers
WSDL
Soap-
lab
Vocabulary
Haystack
Provenance
Browser
Ontology Store
Data descriptions
Scientists

20. myGrid Service Stack Bioinformaticians Tool Providers
Service Providers
Work bench
Taverna
Web Portal
Talisman
Applications
Gateway
Personalisation
Registries
Service and Workflow
Discovery
Provenance
Event Notification
Ontologies
Ontology Mgt
Views
Metadata Mgt
myGrid Information
Repository
Core services
FreeFluo Workflow
Enactment Engine
OGSA-DQP
Distributed Query Processor
services that are the tools that will constitute the experiments, that is: specialised services such as AMBIT text extraction [6], and external third party services such databases, computational analyses, simulations etc, wrapped as web services possibly by SoapLab [2];
services for forming and executing experiments, that is: workflow management services [3], information management services, distributed database query processing [5];
semantic services for discovering services and workflows, and managing metadata, such as: third party service registries and federated personalised views over those registries [8], ontologies and ontology management [13];
services for supporting the e-Science scientific method and best practice found at the bench but often neglected at the workstation, specifically: provenance management [7] and change notification [9].Multiple ways of cutting the architecture.
All the services are web services. Some are grid services (miR andn the DQP) and most will be migrated to rid services (WFEE and event notification)
Bioservices and external services themselves. Web services currently and will become grid services esp. those that are stateful through soaplab.
Some bio services are rendered as ws via soaplab others are not (i.e. those from newcastle).
AMBIt is external web service
Top layer. Apps Workbench, Taverna, Portland Talisman. They use the middle layers through a gateway (fib) which has an overarching view of the myGrid information model.
the User Proxy and Gateway are logically parts of the same thing (i.e. the persistent bit that stands between a paricular user client such as an instance of the workbench and the rest of myGrid), and the User Proxy is still used to support notitications from the workbench and user service selection during workflows (not yet supported in workbench UI) The Gateway per se may not be used by the current version of the workbench since it has yet to be extended to support the newer mIR and enactor designs; i guess that this upgrade will happen between now and all hands. The details of abstract job invocation are currently up in the air since we had our own proprietary job/workflow description schema in the past, but are now trying to unify this with Chris W's emerging stuff and possible scufl extension and broader use of xml schema
Middle payers are the core mygrid services. 5 clusters
Workflow enactment engine
2. DQP
mIR
The e-Science support services: Personalisation, provenance and event notification
Semantics: service/workflow discovery, ontology mgt, metadata mgt + registries and ontologies.
Registries and ontologies could be external
Bottom layer – interest to service providers
Middle layer interest to tool providers
Top layer interest to bioinformaticans
Who build apps for biologists
Web Service (Grid Service) communication fabric
External services
SoapLab
GowLab
Native Web
Services
AMBIT
Text Extraction
Service
Legacy apps
Legacy apps

21. Two+ Paths Innovative work Core functionality
Service and workflow registration
Semantic discovery
Provenance management
Text mining
Core functionality
Services – Soaplab and Gowlab
Workflow enactment engine – Freefluo
Workflow workbench – Taverna
Data integration – OGSADQP
Information model & management
Concentric circles? Reflects on the state of play
In between
Event notification
Gateway

22. myGrid Service Stack Bioinformaticians Tool Providers
Service Providers
Work bench
Taverna
Web Portal
Talisman
Applications
Gateway
Personalisation
Registries
Service and Workflow
Discovery
Provenance
Event Notification
Ontologies
Ontology Mgt
Views
Metadata Mgt
myGrid Information
Repository
Core services
FreeFluo Workflow
Enactment Engine
OGSA-DQP
Distributed Query Processor
services that are the tools that will constitute the experiments, that is: specialised services such as AMBIT text extraction [6], and external third party services such databases, computational analyses, simulations etc, wrapped as web services possibly by SoapLab [2];
services for forming and executing experiments, that is: workflow management services [3], information management services, distributed database query processing [5];
semantic services for discovering services and workflows, and managing metadata, such as: third party service registries and federated personalised views over those registries [8], ontologies and ontology management [13];
services for supporting the e-Science scientific method and best practice found at the bench but often neglected at the workstation, specifically: provenance management [7] and change notification [9].Multiple ways of cutting the architecture.
All the services are web services. Some are grid services (miR andn the DQP) and most will be migrated to rid services (WFEE and event notification)
Bioservices and external services themselves. Web services currently and will become grid services esp. those that are stateful through soaplab.
Some bio services are rendered as ws via soaplab others are not (i.e. those from newcastle).
AMBIt is external web service
Top layer. Apps Workbench, Taverna, Portland Talisman. They use the middle layers through a gateway (fib) which has an overarching view of the myGrid information model.
the User Proxy and Gateway are logically parts of the same thing (i.e. the persistent bit that stands between a paricular user client such as an instance of the workbench and the rest of myGrid), and the User Proxy is still used to support notitications from the workbench and user service selection during workflows (not yet supported in workbench UI) The Gateway per se may not be used by the current version of the workbench since it has yet to be extended to support the newer mIR and enactor designs; i guess that this upgrade will happen between now and all hands. The details of abstract job invocation are currently up in the air since we had our own proprietary job/workflow description schema in the past, but are now trying to unify this with Chris W's emerging stuff and possible scufl extension and broader use of xml schema
Middle payers are the core mygrid services. 5 clusters
Workflow enactment engine
2. DQP
mIR
The e-Science support services: Personalisation, provenance and event notification
Semantics: service/workflow discovery, ontology mgt, metadata mgt + registries and ontologies.
Registries and ontologies could be external
Bottom layer – interest to service providers
Middle layer interest to tool providers
Top layer interest to bioinformaticans
Who build apps for biologists
Web Service (Grid Service) communication fabric
External services
SoapLab
GowLab
Native Web
Services
AMBIT
Text Extraction
Service
Legacy apps
Legacy apps

23. Its turned into a workbench.
Find services dynamically.

24. Viewing intermediate results
Run the Workflow
Viewing intermediate results

25. Run the Workflow

26. Drilling Down: myGrid and Semantics
Workflow and service discovery
Prior to and during enactment
Semantic registration
Workflow assembly
Semantic service typing of inputs and outputs
Provenance of workflows and other entities
Experimental metadata glue
Use of RDF, RDFS, DAML+OIL/OWL
Instance store, ontology server, reasoner
Materialised vs at point of delivery reasoning.
myGrid Information Model

27. Semantic Discovery Pedro data capture tool
Drag a workflow entry into the explorer pane and the workflow loads.
Drag a service/ workflow to the scavenger window for inclusion into the workflow
View annotations on workflow

28. Tutorial focus Innovative work Core functionality
Service and workflow registration
Semantic discovery
Provenance management
Text mining
Core functionality
Services – Soaplab and Gowlab
Workflow enactment engine – Freefluo
Workflow workbench – Taverna
Data integration – OGSADQP
Information model & management
Concentric circles? Reflects on the state of play
In between
Event notification
Gateway

29. Roadmap services workflows workflows data Registry Taverna workbench
1. Describe services
Registry
workflows
2. Discover services
workflows
3. Write & run workflows
Taverna workbench
LSID authorities
data
4. Provenance & data management

30. Sessions on Details Workflows - hands on with Taverna Semantics
Timetable – split sessions
Session 1
Group 1 – hands on (Swanson)
Group 2 – semantics (Newhaven)
Teabreak (short)
Session 2
Group 1 – semantics (Newhaven)
Group 2 –hands on (Swanson)
Discussions and Conclusions

31. Questions? http://www.mygrid.org.uk http://taverna.sf.net